ArticleJournal of structural biology2013
Dynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps.
Article in Journal of structural biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Quantitative mining of compositional heterogeneity in cryo-EM datasets of ribosome assembly intermediates.Structure (London, England : 1993) · 2022Article
- Dynamics and stability in the maturation of a eukaryotic virus: a paradigm for chemically programmed large-scale macromolecular reorganization.Archives of virology · 2021Review
- Assembly of infectious enteroviruses depends on multiple, conserved genomic RNA-coat protein contacts.PLoS pathogens · 2020Article
- Computational Methods for Single-Particle Electron Cryomicroscopy.Annual review of biomedical data science · 2020Review
- Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy.Acta crystallographica. Section F, Structural biology communications · 2019Review
- While the revolution will not be crystallized, biochemistry reigns supreme.Protein science : a publication of the Protein Society · 2017Review
- Structural Study of Heterogeneous Biological Samples by Cryoelectron Microscopy and Image Processing.BioMed research international · 2017Review
- Directly reconstructing principal components of heterogeneous particles from cryo-EM images.Journal of structural biology · 2015Article
- Efficient estimation of three-dimensional covariance and its application in the analysis of heterogeneous samples in cryo-electron microscopy.Structure (London, England : 1993) · 2015Article
- Covariance Matrix Estimation for the Cryo-EM Heterogeneity Problem.SIAM journal on imaging sciences · 2015Article
- Review
- Dynamic and geometric analyses of Nudaurelia capensis ω virus maturation reveal the energy landscape of particle transitions.Journal of molecular recognition : JMR · 2014Article
- Architecture of a dsDNA viral capsid in complex with its maturation protease.Structure (London, England : 1993) · 2014Article
- Bayesian analysis of individual electron microscopy images: towards structures of dynamic and heterogeneous biomolecular assemblies.Journal of structural biology · 2013Article
- Virus assembly and maturation: auto-regulation through allosteric molecular switches.Journal of molecular biology · 2013Review
- Confessions of an icosahedral virus crystallographer.Microscopy (Oxford, England) · 2013Review
Corrections and comments
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Authors and funding
6 authors.
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Abstract
CryoEM data capture the dynamic character associated with biological macromolecular assemblies by preserving the various conformations of the individual specimens at the moment of flash freezing. Regions of high variation in the data set are apparent in the image reconstruction due to the poor density that results from the lack of superposition of these regions. These observations are qualitative and, to date, only preliminary efforts have been made to quantitate the heterogeneity in the ensemble of particles that are individually imaged. We developed and tested a quantitative method for simultaneously computing a reconstruction of the particle and a map of the space-varying heterogeneity of the particle based on an entire data set. The method uses a maximum likelihood algorithm that explicitly takes into account the continuous variability from one instance to another instance of the particle. The result describes the heterogeneity of the particle as a variance to be plotted at every voxel of the reconstructed density. The test, employing time resolved data sets of virus maturation, not only recapitulated local variations obtained with difference map analysis, but revealed a remarkable time dependent reduction in the overall particle dynamics that was unobservable with classical methods of analysis.
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